parsmart.cpp File Reference

#include <openbabel/babelconfig.h>
#include <ctype.h>
#include <iomanip>
#include <cstring>
#include <openbabel/mol.h>
#include <openbabel/atom.h>
#include <openbabel/bond.h>
#include <openbabel/parsmart.h>
#include <openbabel/stereo/stereo.h>
#include <openbabel/stereo/tetrahedral.h>

Namespaces
	OpenBabel

Macros
#define	ATOMPOOL   1
#define	BONDPOOL   1
#define	AE_ANDHI   1
#define	AE_ANDLO   2
#define	AE_OR   3
#define	AE_RECUR   4
#define	AE_NOT   5
#define	AE_TRUE   6
#define	AE_FALSE   7
#define	AE_AROMATIC   8
#define	AE_ALIPHATIC   9
#define	AE_CYCLIC   10
#define	AE_ACYCLIC   11
#define	AE_MASS   12
#define	AE_ELEM   13
#define	AE_AROMELEM   14
#define	AE_ALIPHELEM   15
#define	AE_HCOUNT   16
#define	AE_CHARGE   17
#define	AE_CONNECT   18
#define	AE_DEGREE   19
#define	AE_IMPLICIT   20
#define	AE_RINGS   21
#define	AE_SIZE   22
#define	AE_VALENCE   23
#define	AE_CHIRAL   24
#define	AE_HYB   25
#define	AE_RINGCONNECT   26
#define	AL_CLOCKWISE   1
#define	AL_ANTICLOCKWISE   2
#define	AL_UNSPECIFIED   0
#define	BE_ANDHI   1
#define	BE_ANDLO   2
#define	BE_OR   3
#define	BE_NOT   4
#define	BE_ANY   5
#define	BE_DEFAULT   6
#define	BE_SINGLE   7
#define	BE_DOUBLE   8
#define	BE_TRIPLE   9
#define	BE_QUAD   10
#define	BE_AROM   11
#define	BE_RING   12
#define	BE_UP   13
#define	BE_DOWN   14
#define	BE_UPUNSPEC   15
#define	BE_DOWNUNSPEC   16

Functions
static int	CreateAtom (Pattern *, AtomExpr *, int, int vb=0)
static void	FatalAllocationError (const char *ptr)
static void	FreePattern (Pattern *)
static Pattern *	CopyPattern (Pattern *)
static AtomExpr *	CopyAtomExpr (AtomExpr *expr)
static void	FreeAtomExpr (AtomExpr *expr)
static AtomExpr *	BuildAtomPred (int type)
static AtomExpr *	BuildAtomLeaf (int type, int val)
static AtomExpr *	BuildAtomNot (AtomExpr *expr)
static AtomExpr *	BuildAtomBin (int op, AtomExpr *lft, AtomExpr *rgt)
static AtomExpr *	BuildAtomRecurs (Pattern *pat)
static AtomExpr *	GenerateElement (int elem)
static AtomExpr *	GenerateAromElem (int elem, int flag)
static BondExpr *	CopyBondExpr (BondExpr *expr)
static bool	EquivalentBondExpr (BondExpr *expr1, BondExpr *expr2)
static void	FreeBondExpr (BondExpr *expr)
static BondExpr *	BuildBondLeaf (int type)
static BondExpr *	BuildBondNot (BondExpr *expr)
static BondExpr *	BuildBondBin (int op, BondExpr *lft, BondExpr *rgt)
static BondExpr *	GenerateDefaultBond (void)
static Pattern *	AllocPattern (void)
static int	CreateBond (Pattern *pat, BondExpr *expr, int src, int dst)
static void	MarkGrowBonds (Pattern *pat)
static int	GetChiralFlag (AtomExpr *expr)
static int	GetExprOrder (BondExpr *expr)
static int	GetExprCharge (AtomExpr *expr)
static int	GetExprAtomicNum (AtomExpr *expr)
void	SmartsLexReplace (std::string &s, std::vector< std::pair< std::string, std::string > > &vlex)

Variables
const int	SmartsImplicitRef = -9999

Detailed Description

Implementation of Daylight SMARTS parser.

Macro Definition Documentation

ATOMPOOL

#define ATOMPOOL   1

Referenced by OpenBabel::CreateAtom().

BONDPOOL

#define BONDPOOL   1

Referenced by OpenBabel::CreateBond().

AE_ANDHI

#define AE_ANDHI   1

Referenced by OpenBabel::CopyAtomExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OpenBabel::GetChiralFlag(), OpenBabel::GetExprAtomicNum(), OpenBabel::GetExprCharge(), and OBSmartsPattern::ParseAtomExpr().

AE_ANDLO

#define AE_ANDLO   2

Referenced by OpenBabel::CopyAtomExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OpenBabel::GetChiralFlag(), OpenBabel::GetExprAtomicNum(), OpenBabel::GetExprCharge(), and OBSmartsPattern::ParseAtomExpr().

AE_OR

#define AE_OR   3

Referenced by OpenBabel::CopyAtomExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), OpenBabel::GetChiralFlag(), OpenBabel::GetExprAtomicNum(), OpenBabel::GetExprCharge(), and OBSmartsPattern::ParseAtomExpr().

AE_RECUR

#define AE_RECUR   4

Referenced by OpenBabel::BuildAtomRecurs(), OpenBabel::CopyAtomExpr(), OBSmartsMatcher::EvalAtomExpr(), and OpenBabel::FreeAtomExpr().

AE_NOT

#define AE_NOT   5

Referenced by OpenBabel::BuildAtomNot(), OpenBabel::CopyAtomExpr(), OBSmartsMatcher::EvalAtomExpr(), OpenBabel::FreeAtomExpr(), and OpenBabel::GetChiralFlag().

AE_TRUE

#define AE_TRUE   6

Referenced by OBSmartsMatcher::EvalAtomExpr(), OBSmartsPattern::ParseComplexAtomPrimitive(), and OBSmartsPattern::ParseSimpleAtomPrimitive().

AE_FALSE

#define AE_FALSE   7

Referenced by OBSmartsMatcher::EvalAtomExpr().

AE_AROMATIC

#define AE_AROMATIC   8

Referenced by OBSmartsMatcher::EvalAtomExpr(), OBSmartsPattern::ParseComplexAtomPrimitive(), and OBSmartsPattern::ParseSimpleAtomPrimitive().

AE_ALIPHATIC

#define AE_ALIPHATIC   9

Referenced by OBSmartsMatcher::EvalAtomExpr(), OBSmartsPattern::ParseComplexAtomPrimitive(), and OBSmartsPattern::ParseSimpleAtomPrimitive().

AE_CYCLIC

#define AE_CYCLIC   10

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_ACYCLIC

#define AE_ACYCLIC   11

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_MASS

#define AE_MASS   12

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_ELEM

#define AE_ELEM   13

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GenerateElement(), and OpenBabel::GetExprAtomicNum().

AE_AROMELEM

#define AE_AROMELEM   14

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GenerateAromElem(), and OpenBabel::GetExprAtomicNum().

AE_ALIPHELEM

#define AE_ALIPHELEM   15

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GenerateAromElem(), and OpenBabel::GetExprAtomicNum().

AE_HCOUNT

#define AE_HCOUNT   16

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_CHARGE

#define AE_CHARGE   17

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GetExprCharge(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_CONNECT

#define AE_CONNECT   18

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_DEGREE

#define AE_DEGREE   19

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_IMPLICIT

#define AE_IMPLICIT   20

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_RINGS

#define AE_RINGS   21

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_SIZE

#define AE_SIZE   22

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_VALENCE

#define AE_VALENCE   23

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_CHIRAL

#define AE_CHIRAL   24

Referenced by OBSmartsMatcher::EvalAtomExpr(), OpenBabel::GetChiralFlag(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_HYB

#define AE_HYB   25

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AE_RINGCONNECT

#define AE_RINGCONNECT   26

Referenced by OBSmartsMatcher::EvalAtomExpr(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AL_CLOCKWISE

#define AL_CLOCKWISE   1

Referenced by OpenBabel::GetChiralFlag(), OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AL_ANTICLOCKWISE

#define AL_ANTICLOCKWISE   2

Referenced by OpenBabel::GetChiralFlag(), OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().

AL_UNSPECIFIED

#define AL_UNSPECIFIED   0

Referenced by OBSmartsMatcher::match(), and OBSmartsPattern::ParseComplexAtomPrimitive().

BE_ANDHI

#define BE_ANDHI   1

Referenced by OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::FreeBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondExpr().

BE_ANDLO

#define BE_ANDLO   2

Referenced by OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::FreeBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondExpr().

BE_OR

#define BE_OR   3

Referenced by OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalBondExpr(), OpenBabel::FreeBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondExpr().

BE_NOT

#define BE_NOT   4

Referenced by OpenBabel::BuildBondNot(), OpenBabel::CopyBondExpr(), OpenBabel::EquivalentBondExpr(), OBSmartsMatcher::EvalBondExpr(), and OpenBabel::FreeBondExpr().

BE_ANY

#define BE_ANY   5

Referenced by OBSmartsMatcher::EvalBondExpr(), and OBSmartsPattern::ParseBondPrimitive().

BE_DEFAULT

#define BE_DEFAULT   6

Referenced by OBSmartsMatcher::EvalBondExpr(), and OpenBabel::GenerateDefaultBond().

BE_SINGLE

#define BE_SINGLE   7

Referenced by OBSmartsMatcher::EvalBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondPrimitive().

BE_DOUBLE

#define BE_DOUBLE   8

Referenced by OBSmartsMatcher::EvalBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondPrimitive().

BE_TRIPLE

#define BE_TRIPLE   9

Referenced by OBSmartsMatcher::EvalBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondPrimitive().

BE_QUAD

#define BE_QUAD   10

Referenced by OBSmartsMatcher::EvalBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondPrimitive().

BE_AROM

#define BE_AROM   11

Referenced by OBSmartsMatcher::EvalBondExpr(), OpenBabel::GetExprOrder(), and OBSmartsPattern::ParseBondPrimitive().

BE_RING

#define BE_RING   12

Referenced by OBSmartsMatcher::EvalBondExpr(), and OBSmartsPattern::ParseBondPrimitive().

BE_UP

#define BE_UP   13

Referenced by OpenBabel::GetExprOrder().

BE_DOWN

#define BE_DOWN   14

Referenced by OpenBabel::GetExprOrder().

BE_UPUNSPEC

#define BE_UPUNSPEC   15

Referenced by OpenBabel::GetExprOrder().

BE_DOWNUNSPEC

#define BE_DOWNUNSPEC   16

Referenced by OpenBabel::GetExprOrder().